Author Archives: Bryant Rathbone

Kill The Winner

What We Don’t See At Sea

When we are taught about the ocean’s food chain in elementary school, it seems simple enough. The tiny plankton at the bottom are the primary producers, equivalent to the plants on land, and everything gets bigger and more interesting from there.

The layman's ocean food chain

Figure 1. The Layman's Ocean Food Chain

In fact, plankton themselves hold an enormous amount of diversity. The term “plankton” include not just plants, but every kingdom of life. Huge diversity exists within each kingdom as well, multiple species fill each ecological niche in each environment (1).

Now, that level of diversity may seem odd. For one ecological niche in one environment, shouldn’t one species come to dominate? One would think that one species would prove best able to grow in the environment, take up the most nutrients and crowd out its competitors. Yet this diversity still exists.

For oceanic bacteria at least, the reason seems to be that they are trapped in a bitter conflict, a race between their own rate of replication and how quickly their tormentors destroy them. It is a war between bacteria and viruses, one which kills as many as 50% of the ocean’s bacteria every day (2).

Killing The Winner

The Blue Shell (Nintendo Corp.)

How does this explain the level of bacterial diversity? Bacteria must find a balance between their own success and avoiding eradication by viruses. Traditionally, an organism is considered  most successful when it grows to reach the highest population that its environment can support.

Viruses usually prey on only one species. A bacterium that has achieved complete success has made itself completely vulnerable to its viruses. In a dense population of its target species, a virus will spread like wildfire, and is much more likely to completely eliminate its prey (1). This concept is called “kill the winner.”

With population density limited in this way, there is room for other species to move into the same niche in the same environment, although it may not be as well suited as its competitor. So long as no one species reaches a density that allows a runaway viral infection, it will survive.

The ecological niche still supports a maximum number of organisms, but viruses kill the winner, ensuring a diversity of species in the same niche.

To help to illustrate the relationship between rates of infection and population density, adjust the population of this zombie apocalypse model using the + and – keys. Note that when the population is dense, the infection spreads much more quickly. If the humans start off winning, they lose very quickly.

Unlike the survivors in this simulation, bacteria can replace themselves, allowing a sustained population. Between rates of replication and death by infection, each bacterial species must find a way to succeed as best as it is able.

References

(1) Fuhrman, J. A.; Schwalbach, M.: Viral Influence on Aquatic Bacterial Communities Biol. Bull. 2003204, 192.

(2) The Annenberg Foundation: The Habitable Planet. http://www.learner.org/courses/envsci/index.html (accessed 03/12, 2012).

Doing It The Old Fashioned Way

It’s a nightmare scenario to modern science students: facing a physics midterm with a dead calculator. We have all used these miniature computers so extensively in learning math that most of us don’t trust ourselves to do it any other way.

We are all aware that there must have been some stygian era before these wonderful devices came into existence. Calculations must all have been carried out manually. This is not the case. Before there were digital computers, there were analog computers.

The first known analog computer was manufactured around 100 BC. This device, known as the Antikythera mechanism, was used by ancient Greek astronomers to predict the movement of celestial bodies.

A fragment of the Antikythera mechanism. Source: computus.org

Analog computers reached their most advanced forms in the 1950s, when they were used in to aim the weapons of naval vessels. This may seem counter-intuitive; artillery problems are used to teach some of the simplest concepts in first-year physics, surely this could be done by hand. Bear in mind, these simple artillery problems have only two dimensions and involve stationary targets and stationary firing platforms all operating in a frictionless vacuum.

The real world is so much more complex than these problems that fire-control computers accepted as many as 25 variables. For comparison, the simplest kinematics problems have 5 variables. A mathematician could do the same calculation in minutes, at best, and only then for one selected instant. Fire-control required continuous output under constantly changing conditions.

While the history of these devices is interesting, how do they work? To illustrate the basic principle, we’ll construct a very simple analog computer.

For illustrative purposes, our goal will be simple, to divide by two. We will call our known, or input, variable y and our unknown, or output, x. The function calculated is:

 y=2x

To start we have two wheels, which could just as easily be gears, designated A and B.

Public domain

Wheel A has a diameter of 1, wheel B has a diameter of 2. Since circumference is the diameter multiplied by pi, if the outside edge of A were flattened out, it would be half the length of the similarly flattened edge of B. When A turns once, it will roll along half the edge of B, driving a half revolution of B.

Public domain

The revolutions of A represent the input and the revolutions of B represent the output. Six turns of A will produce three turns of B, just as 6/2=3.

To make input and the reading of output easier, we can label the inputs and outputs on the wheels. For simplicity, only a few outputs are labelled, but high resolution can be achieved with the same principle.

Public domain

Here, we see that the input and, consequently, the output, are zero. Rotating A 90 degrees, rotates B 45, so that the input of 2, gives an output of 1.

Public domain

Analog computers have many more complex mechanisms, but the guiding principle is the same; displacement or rotation of components used to model variable values.

This 6 part training film outlines this and many more mechanisms used in mechanical computers.

YouTube Preview Image

References

(1) The Antikythera Mechanism Project The Antikythera Mechanism Project. http://www.antikythera-mechanism.gr/ (accessed 02/12, 2012).

(2) Navy Dept. Bureau of Ordnance In Basic Fire Control Mechanisms; Ford Instrument Co. Inc.: Long Island City, NY, 1944; , pp 425.

SCIE 300 Scientific Investigation Project: The value of good taste

Rachel Lee, Bryant Rathbone, Colin Todd

PowerPoint slides (link)

References

(1) Brentari, E.; Levaggi, E. Food Quality and Preference 2011, 22, 725-732.

(2) Brochet, F.; Dubourdieu, D. Brain and Language 2001, 77, 187-196.

(3) Gawel, R. Journal of Sensory Studies 1997, 12, 267-284.

(4) Goldstein, R.; Almenberg, J.; Dreber, A.; Emerson, J. W.; Herschkowitsch, A.; Katz, J. Journal of Wine Economics 2008, 3, 1-9.

(5) Harris, L. C.; Cai, K. Y. Journal of Market-Focused Management 2002, 5, 171.

(6) Hughson, A.; Ashman, H.; De La Huerga, V.; Moskowitz, H. JOURNAL OF SENSORY STUDIES 2004, 19, 85-105.

(7) Kumar, N.; Scheer, L.; Kotler, P. European Management Journal 2000, 18, 129.

(8) Laoro, M.; Delahunty, C.; Cox, D. Food Research International , 44, 3235.

(9) LaTour, K. A.; LaTour M.S.; Feinstein A.H. Cornell Hospitality Quarterly 2011, 52, 445.

(10) Lawless, H. Journal of Food Science 1984, 49, 120-123.

(11) Lehrer, J. The Subjectivity of Wine. http://scienceblogs.com/cortex/2007/11/the_subjectivity_of_wine.php (accessed 01/17, 2012).

(12) MacQueen, K. MacLeans 2011, .

(13) Mckinnon, M. The Globe and Mail 2011, .

(14) Morrot, G.; Brochet, F.; Dubourdieu, D. Brain and Language 2001, 79, 309-320.

(15) Solomon, G. American Journal of Psychology 1990, 105, 495-517.